Epub or PDF reader with Synch?

This is my first ever post, so I hope I'm doing it in the right place.

I love, love, love how the Nook and Kindle apps let me synch among my ebooks when I read in different devices. The problem is that it only works with books I buy from them. Is there any app out there that will allow me to synch my own pdfs or ebooks? I heard that Comicrack does something like that, but it works only with comic formats.

Well, that is a general problem with PDF reader. The better reader have the option of reflowed text. This works with text-only books properly.
But often I read technical docs like manuals which have pics and drawings. Reflow text mode puts these at other places or even all together at the end of the doc.

But Kindle should have a reflow text mode at least, there Kindle has room for improvement